a. Field of the Invention
The invention relates generally to the field of microscopic organism detection, and more particularly to the detection of microscopic organisms utilizing bacteriophage or other like viral organisms.
b. Statement of the Problem
Standard microbiological methods for detection of microorganisms have relied on substrate-based assays to test for the presence of specific bacterial pathogens. See Robert H. Bordner, John A. Winter, and Pasquale Scarpino, Microbiological Methods For Monitoring The Environment, EPA Report No. EPA-600/8-78-017, U.S. Environmental Protection Agency, Cincinnati, Ohio, 45268, December 1978. These techniques are generally easy to perform, do not require expensive supplies or laboratory facilities, and offer high levels of selectivity. However, substrate-based assay methods are slow, requiring the growth and cultivation of pure cultures of the targeted organism on appropriate substrate. The growth period can take as long as twenty-four hours and in some cases longer. This time constraint severely limits the effectiveness of substrate-based assays to provide rapid response to the presence of virulent strains of microorganisms.
Molecular biology based techniques are quickly gaining acceptance as valuable alternatives to standard microbiological tests like the substrate-based assay. Serological methods have been widely employed to evaluate a host of matrices for targeted microorganisms. See David T. Kingsbury and Stanley Falkow, Rapid Detection And Identification of Infectious Agents, Academic Press, Inc., New York, 1985 and G. M. Wyatt, H. A. Lee, and M. R. A. Morgan, Chapman & Hall, New York, 1992. These tests focus on using antibodies to first trap and then separate targeted organisms from other constituents in complicated biological mixtures. Once isolated, the captured organism can be concentrated and detected by a variety of different techniques that do not require cultivating the biological analyte. One such approach, termed “immunomagnetic separation” (IMS), involves immobilizing antibodies to spherical, micro-sized magnetic or paramagnetic beads and using these beads to trap targeted microorganisms from liquid media. The beads are easily manipulated under the influence of a magnetic field facilitating the retrieval and concentration of targeted organisms. Moreover, the small size and shape of the beads allow them to become evenly dispersed in the sample, accelerating the rate of interaction between bead and target. These favorable characteristics lead to reductions in assay time and help streamline the analytical procedure, making it more applicable for higher sample throughput and automation.
Downstream detection methods previously used with IMS include ELISA (Kofitsyo S. Cudjoe, Therese Hagtvedt, and Richard Dainty, “Immunomagnetic Separation of Salmonella From Foods And Their Detection Using Immunomagnetic Particle”, International Journal of Food Microbiology, 27 (1995), pp. 11-25), dot blot assay (Eystein Skjerve, Liv Marit Rorvik, and Orjan Olsvick, “Detection Of Listeria Monocytogenes In Foods By Immunomagnetic Separation”, Applied and Environmental Microbiology, November 1990, pp. 3478-3481), electrochemiluminescence (Hao Yu and John G. Bruno, Immunomagnetic-Electrochemiluminescent Detection Of Escherichia coli 0157 and Salmonella typhimurium In Foods and Environmental Water Samples”, Applied and Environmental Microbiology, February 1996, pp. 587-592), and flow cytometry (Barry H. Pyle, Susan C. Broadway, and Gordon A. McFeters, “Sensitive Detection of Escherichia coli O157:H7 In Food and Water By Immunomagnetic Separation And Solid-Phase Laser Cytometry”, Applied and Environmental Microbiology, May 1999, pp. 1966-1972). Although these tests provide satisfactory results, they are laborious to perform and give binary responses (yes/no) that are highly susceptible to false-positive results due to cross-reactivity with non-target analytes. Another method for identifying whole cellular microorganisms uses IMS coupled to matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) (Holland et al., 1996; van Barr, 2000; Madonna et al., 2000).
These alternative approaches can offer faster results than do traditional microbiology based methods. However, they do not achieve the sensitivity levels that substrate-based assays do, are more expensive, and typically require more highly trained technicians than do classical substrate-based methods.
Other molecular biology techniques have received a great deal of recent attention toward microorganism detection, including Polymerase Chain Reaction (PCR). PCR detection of specific microorganisms in a sample involves extraction of the genetic material (RNA and/or DNA) in a sample, amplification of a target genetic sequence specific to the microorganism of interest, and then detection of the amplified genetic material. PCR techniques offer high selectivity owing to the uniqueness of the detected genetic material, high sensitivity because of the substantial amplification of the target genetic material, and rapid results owing to the potentially fast amplification process. However, PCR instruments and reagents are quite expensive and highly trained technicians are needed to perform the tests.
Some attempts have been made to improve upon substrate-based classical bacterial detection methods using bacteriophage infection and amplification. Bacteriophages are viruses that have evolved in nature to use bacteria as a means of replicating themselves. A bacteriophage (or phage) does this by attaching itself to a bacterium and injecting its genetic material into that bacterium, inducing it to replicate the phage from tens to thousands of times. Some bacteriophage, called lytic bacteriophage, rupture the host bacterium releasing the progeny phage into the environment to seek out other bacteria to infect. The total incubation time for phage infection of a bacterium, phage multiplication (amplification) in the bacterium, and release of the progeny phage after lysis can take as little as an hour depending on the phage, the bacterium, and the environmental conditions. Microbiologists have isolated and characterized over 5,000 phage species, including many that specifically target bacteria at the species or even the strain level. U.S. Pat. No. 5,985,596 issued Nov. 16, 1999 to Stuart Mark Wilson and U.S. Pat. No. 6,461,833 B1 issued Oct. 8, 2002 to Stuart Mark Wilson describe such a phage-based assay method. It comprises a lytic phage infection of a sample that may contain bacteria of interest. This is followed by removal of free phage from the sample, target bacteria lysis, and then infection of a second bacterium by the progeny phage where the second bacterium has a shorter doubling time than does the target bacterium. The prepared sample is grown on a substrate and the formation of plaques indicates the presence of the target bacterium in the original sample. This method can shorten the assay time of a traditional substrate-based assay, though assays still take many hours or days because of the requisite culture incubation times. Another problem with the method is that it can only be applied to detect bacterium for which a non-specific phage exists that also infects a more rapidly doubling bacterium than the target bacterium. Usage of a nonspecific phage opens the possibility of cross-reactivity to at least the second bacterium in test samples. Thus, this phage-based, plaque assay method is not rapid, can only be applied if a suitable non-specific phage is available, is prone to cross-reactivity problems, and must be performed in a lab setting.
Other bacterial pathogen detection methods utilize bacteriophage that have been genetically modified with detectable marker or reporter marker genes which is only expressed if a target bacterium is present in a sample and is then infected by the modified phage. U.S. Pat. No. 4,861,709 issued Aug. 29, 1989 to Ulitzur et al. is a typical example. A phage that specifically infects a target pathogen is modified to include a lux gene. When the modified phage is added to a sample containing the target bacterium, the phage infects the bacterium, luciferase is produced in the bacterium, and light is emitted. U.S. Pat. No. 5,824,468 issued Oct. 20, 1998 to Scherer et al. describes a similar method. In addition to luciferase-producing gene markers, Scherer et al. describes gene markers that are expressed as detectable proteins or nucleic acids. U.S. Pat. No. 5,656,424 issued Aug. 12, 1997 to Jurgensen et al. describes a method utilizing luciferase (or β-galactosidase) reporter phage to detect mycobacteria. It further describes testing for antibiotic susceptibility. U.S. Pat. No. 6,300,061 B1 issued Oct. 9, 2001 to Jacobs, Jr. et al. describes yet another method for detecting mycobacteria using genetically modified phage, which produces one of several reporter molecules after bacterial infection, including luciferase. U.S. Pat. No. 6,555,312 B1 issued Apr. 29, 2003 to Hiroshi Nakayama describes a method utilizing a gene that produces a fluorescent protein marker rather than a luminescent one. All of these methods take implicit advantage of phage amplification within infected bacteria. For each target bacterium infected in a sample, the marker gene is expressed many times over as the progeny phage are produced. U.S. Pat. No. 6,544,729 B2 issued Apr. 8, 2003 to Sayler et al. adds an additional amplification process. A phage's DNA is modified to include a lux gene. A bioreporter cell is also modified to include a lux gene. The genetically modified phage and bioreporter cells are added to a sample. If the phage infects target bacteria, the target bacteria are induced to produce not only luciferase but also acyl en homoserine lactone N-(3-oxohexanoyl) homoserine lactone (AHL). AHL finds its way into the bioreporter cells, stimulating the production of additional light and additional AHL, which in turn finds its way into additional bioreporter cells resulting in the production of even more light. Thus, an amplified light signal is triggered by the phage infection of the target bacteria. In principle, all of these methods utilizing genetically modified phage make possible: 1) high selectivity because they utilize selectively infecting phage; 2) high sensitivity because the marker gene products can be detected at low levels; and 3) results that are faster than substrate-based methods because the signal can be detected within one or two phage infection cycles. They have two potential drawbacks: first, they are expensive and can be difficult to implement because suitable phage must be genetically modified for each pathogen to be tested; and second, they often require an instrument to detect the marker signal (light), driving up the cost of tests utilizing genetically modified phage.
U.S. Pat. No. 5,888,725 issued Mar. 30, 1999 to Michael F. Sanders describes a method utilizing unmodified, highly specific lytic phages to infect target bacteria in a sample. Phage-induced lysis releases certain nucleotides from the bacterial cell such as ATP that can be detected using known techniques. Detecting increased nucleotide concentrations in a sample after phage infection indicates the presence of target bacteria in the sample. U.S. Pat. No. 6,436,661 B1 issued Aug. 20, 2002 to Adams et al. describes a method whereby a phage is used to infect and lyse a target bacterium in a sample releasing intracellular enzymes, which react in turn with an immobilized enzyme substrate, thereby producing a detectable signal. While these methods have the advantage of using unmodified phage, they do not derive any benefit from phage amplification. The concentration of detected markers (nucleotides or enzymes) is directly proportional.
U.S. Pat. No. 5,498,525 issued Mar. 12, 1996 to Rees et al. describes a pathogen detection method using unmodified phage and phage amplification to boost the detectable signal. The method calls for adding a high concentration of a lytic phage to a sample. The sample is incubated long enough to allow the phage to infect the target bacteria in the sample. Before lysis occurs, the sample is treated to remove, destroy, or otherwise inactivate the free phage in the sample without affecting the progeny phage being replicated within infected bacteria. If necessary, the sample is subsequently treated to neutralize the effects of any anti-viral agent previously added to the sample. The progeny phage released by lysis are detected using a direct assay of the progeny phage or by using a genetically modified bioreporter bacterium to generate a signal indicating the presence of progeny phage in the sample. In either case, the measured signal is proportional to the number of progeny phage rather than the number of target bacteria in the original sample and, thus, is enhanced as a result of phage amplification. One disadvantage of this method is that it requires free phage in the treated sample to be destroyed, removed, or inactivated followed by reversal of the virucidal conditions such that progeny phage will remain viable after lysis. These additional processes complicate assays utilizing the method and make them more expensive.
What is needed in the art is a detection method combining the sensitivity, simplicity, and/or low cost of substrate-based assays with the rapid results offered by molecular biology diagnostic tests.
Against this backdrop the present invention has been developed.